SMTL ID : 8cga.1

Structure of Mycobacterium tuberculosis dUTPase delta 133A-137S mutant

Coordinates

PDB Format Compare

Method

X-RAY DIFFRACTION 1.30 Å

Oligo State

homo-trimer

Ligands

3 x DUP: 2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE(Non-covalent)

DUP.1: 15 residues within 4Å: Chain A: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Chain B: R.84, S.85, G.86, Q.133 Chain C: R.155 Ligands: MG.7 23 PLIP interactions: 10 interactions with chain A, 2 interactions with chain C, 11 interactions with chain B Hydrophobic interactions: A:Y.106 Hydrogen bonds: A:N.97, A:D.103, A:D.103, A:Y.106, A:K.111, A:K.111, C:R.155, B:R.84, B:R.84, B:S.85, B:S.85, B:G.86, B:Q.133 Water bridges: A:T.101, A:A.113, A:A.113, B:R.90, B:R.130, B:R.130, B:Q.133 Salt bridges: C:R.155, B:R.84 DUP.6: 15 residues within 4Å: Chain A: R.155 Chain B: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Chain C: R.84, S.85, G.86, Q.133 Ligands: MG.12 23 PLIP interactions: 2 interactions with chain A, 10 interactions with chain B, 11 interactions with chain C Hydrogen bonds: A:R.155, B:N.97, B:D.103, B:D.103, B:Y.106, B:K.111, B:K.111, C:R.84, C:R.84, C:S.85, C:S.85, C:G.86, C:Q.133 Salt bridges: A:R.155, C:R.84 Hydrophobic interactions: B:Y.106 Water bridges: B:T.101, B:A.113, B:A.113, C:R.90, C:R.130, C:R.130, C:Q.133 DUP.11: 15 residues within 4Å: Chain A: R.84, S.85, G.86, Q.133 Chain B: R.155 Chain C: N.97, G.100, T.101, I.102, D.103, Y.106, E.109, I.110, K.111 Ligands: MG.2 23 PLIP interactions: 11 interactions with chain A, 2 interactions with chain B, 10 interactions with chain C Hydrogen bonds: A:R.84, A:R.84, A:S.85, A:S.85, A:G.86, A:Q.133, B:R.155, C:N.97, C:D.103, C:D.103, C:Y.106, C:K.111, C:K.111 Water bridges: A:R.90, A:R.130, A:R.130, A:Q.133, C:T.101, C:A.113, C:A.113 Salt bridges: A:R.84, B:R.155 Hydrophobic interactions: C:Y.106

3 x MG: MAGNESIUM ION(Non-functional Binders)

MG.2: 1 residues within 4Å: Ligands: DUP.11 No protein-ligand interaction detected (PLIP) MG.7: 1 residues within 4Å: Ligands: DUP.1 No protein-ligand interaction detected (PLIP) MG.12: 1 residues within 4Å: Ligands: DUP.6 No protein-ligand interaction detected (PLIP)

3 x SO4: SULFATE ION(Non-functional Binders)

SO4.3: 2 residues within 4Å: Chain A: G.33, R.127 2 PLIP interactions: 2 interactions with chain A Hydrogen bonds: A:G.33 Salt bridges: A:R.127 SO4.8: 2 residues within 4Å: Chain B: G.33, R.127 2 PLIP interactions: 2 interactions with chain B Hydrogen bonds: B:G.33 Salt bridges: B:R.127 SO4.13: 2 residues within 4Å: Chain C: G.33, R.127 2 PLIP interactions: 2 interactions with chain C Hydrogen bonds: C:G.33 Salt bridges: C:R.127

3 x GOL: GLYCEROL(Non-functional Binders)

GOL.4: 3 residues within 4Å: Chain A: R.29, P.35, L.36 4 PLIP interactions: 4 interactions with chain A Hydrogen bonds: A:R.29, A:R.29, A:L.36, A:L.36 GOL.9: 3 residues within 4Å: Chain B: R.29, P.35, L.36 4 PLIP interactions: 4 interactions with chain B Hydrogen bonds: B:R.29, B:R.29, B:L.36, B:L.36 GOL.14: 3 residues within 4Å: Chain C: R.29, P.35, L.36 4 PLIP interactions: 4 interactions with chain C Hydrogen bonds: C:R.29, C:R.29, C:L.36, C:L.36

3 x TRS: 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL(Non-functional Binders)

TRS.5: 13 residues within 4Å: Chain A: S.94, I.95, V.96, L.117 Chain B: S.94, I.95, V.96 Chain C: S.94, I.95, V.96, L.117 Ligands: TRS.10, TRS.15 8 PLIP interactions: 4 interactions with chain B, 2 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.94, B:I.95, C:S.94, A:S.94 Water bridges: B:S.94, B:I.95, C:S.94, A:I.95 TRS.10: 13 residues within 4Å: Chain A: S.94, I.95, V.96, L.117 Chain B: S.94, I.95, V.96, L.117 Chain C: S.94, I.95, V.96 Ligands: TRS.5, TRS.15 8 PLIP interactions: 2 interactions with chain B, 4 interactions with chain C, 2 interactions with chain A Hydrogen bonds: B:S.94, C:S.94, C:I.95, A:S.94 Water bridges: B:I.95, C:S.94, C:I.95, A:S.94 TRS.15: 13 residues within 4Å: Chain A: S.94, I.95, V.96 Chain B: S.94, I.95, V.96, L.117 Chain C: S.94, I.95, V.96, L.117 Ligands: TRS.5, TRS.10 8 PLIP interactions: 2 interactions with chain C, 2 interactions with chain B, 4 interactions with chain A Hydrogen bonds: C:S.94, B:S.94, A:S.94, A:I.95 Water bridges: C:I.95, B:S.94, A:S.94, A:I.95

Links

RCSB   PDBe   PDBe-KB   PDBj   PDBsum   CATH   PLIP

Citation

Toth, Z.S. et al., The homodimerization domain of the Stl repressor is crucial for efficient inhibition of mycobacterial dUTPase. Sci Rep (2024)

Release Date

2024-05-15

Peptides

Deoxyuridine 5'-triphosphate nucleotidohydrolase: ABC

SMTL:PDB

SMTL Chain Id:
PDB Chain Id:

A
A

B
A

C
A

Deoxyuridine 5'-triphosphate nucleotidohydrolase